Hello all. This is a tricky problem to explain. I'll try my best to articulate what's happening.

This project involves two stages of pre-comps before being loaded into the master comp. The steps are as follows.

Pre comp 1: A basic animation

Pre comp 2: Time Remapping

Master comp: Run for the duration of Pre comp 2

In one of my set ups, I have a .png image of a stack of up-right books (sketched and exported from Illustrator). Pre comp 1 contains an animation of the books falling over. It's one second in duration. I then load Pre comp 1 (1 second in length) into Pre comp 2 (5 seconds). Using Time Remap, I hold the inital frame of Precomp 1 for 2 seconds, let the animation play for it's normal length of time (1 second), and then hold the last frame for the remaining 2 seconds. Nothing tricky is done with the Time Remap (no expressions and no loops). I loaded Pre comp 2 into the Master comp. In the Master comp, I have Pre comp 2 positioned off screen. It moves into sight right as the books fall over and holds for two more seconds before I have it's opacity setting set to 0%. Everything worked great when I did the initial set up.

Here is the problem: On a different day, I reloaded my project and wanted to make some changes. I noticed that my Pre comp 2 was disappearing prematurely (i.e. before its opacity begins to decline from 100%). I checked Pre comp 2 thinking that my time remapping was incorrect. It turns out it worked just fine except that it would also disappear after about 3 seconds. There are no opacity setting changes in Pre comp 2, so I moved to Pre comp 1. In Precomp1, everything disappears prematurely at exactly the same time. I don't see any settings that are making these objects disappear. I've even checked my layer positioning to make sure everything was in order and it was.

I found that if I changed the opacity of the first layer in Pre comp 1 from 100% to 99% everything works correctly. I don't understand why this would fix the problem and don't understand what happened to cause it. Any ideas?

Yes, It's in CS6. I turned the opacity in Pre comp 1 back to 100% from 99% to see what would happen. I purged all memory cache and found that my Pre comp 1 worked just fine, but then the Master Comp had disappearing issues. I emptied the disk cache and all the problems came right back. Changing it back to 99% fixes all the problems

I would be more than happy to send you the proj file, but the more I toy around with it the more I believe it is the cache, even though your initial solution didn't quite fix it. As I got closer to finishing the project, more and more little bugs like this began to occur (maybe about 2 or 3 times in the past 4 hours or so?) and a cache clean up fixes them. A new problem emerged where I cannot render the master comp past 20 secs and 15 frames. I checked the easy things (checked work space, made sure I'm using the right commands, etc.) but still no progress. I can shrink my work space down to the area that's not rendering and it will render just fine, but then the memory clears up in other portions of the comp (the little green bar almost completely disappears with the exception of a few blue spots). It could just be my system too.

If you would still like to see the project file, I can send it to you via email. And yes, once I'm 100% completed, I'll file a bug report

Update on the rendering issue. I increased the amount of ram all my adobe products can use from 6 GBs to 6.5 and the amount being rendered increased by a few seconds. Sounds like it could be a system problem